daadams, I think you'll come out of this fine, although I also don't know if/why you really needed a new ECM. It (new ECM) may be needed as part of the fuel pump "move" but that's just a guess. They may be working from a TSB. Glad you're warranty was still in effect.
Although it's a royal pain to service, having the pump in the tank is the best place for it, at least for a stock setup. That's where you have the highest "head" pressure to the pump which reduces the work the pump has to do, and also reduces the amount of air, mixed into the fuel, downstream of the pump. It's also a good way to keep the pump "cool" although I suspect it simply allows them to just use an even "cheaper" pump.
The so-called "lift pump" has always been a bad or at least a weak method for (stock) fuel delivery to the injector pump. Aftermarket systems from Glacier, FASS, etc. use a much higher capacity pump which encourages the always present air to end up in the return line. They do "lift" fuel, meaning they are "above" the fuel/air line in the tank, however the volume of fuel reaching the return point is much higher therefore most of the air ends up going back to the tank. The increased pressure also makes it possible to place a much better filter ahead of the injector pump.
What "probably" happened to you is your flow rate to the filter head was low enough that you had little, if any, return flow back to the tank. Your injector pump can actually pull its own fuel from the tank but has no means to remove the air, which should happen in the stock filter assembly. Eventually there is enough air around the filter that as you turn, accelerate, or go up/down steep hills that it (the bubble) covers the pick up tube, thus starving the injector pump, which is "hard" on the CP3 and "catastrophic" on the VP44. It's actually an extremely un-complicated condition... meaning... if you stall or sputter in turns, etc. , well... you're probably "pulling" air. Since you are always "pushing" air somewhere, then that means you are failing to "remove" it somewhere in between...
Long story, short version... improving fuel "delivery" to the injector pump is probably one of the best investments you can make since it not only reduces outright failures, it also reduces some normal wear and tear on the injector pump and the injectors themselves. It can also potentially improve your mileage and performance by removing even more of the "normal" air before it reaches the injection pump.
Last but not least... Don't worry too much about so-called "trash" in your fuel. I replaced my own ('06) in-tank pump at about 180K and there was almost zero "trash" in the tank... not even enough to soil a single paper towel. There was exponentially more debris in the bottom of the pump "assembly" and most of that was tiny metalic slivers which are an un-avoidable by-product of any high capacity fuel station (from their own pumps, valves, nozzels, etc. ). As long as you buy fuel at a reputable location and take care of your own truck, "trash" is mostly "myth"...
FWIW, I am not a vendor or rep. I haven't even taken my own advice here... yet. Still relying on, and worrying about, my in-tank pump. However, with an aux tank, I rarely let my stock tank fall below 10 gallons and try to keep it at 25+ (better cooling + less sloshing/air). Yet another reason I love my T-Flo tank/Trax-II setup. I also have a 2u filter between the tanks and only add fuel at the aux tank so the stock system stays very clean and dry, end to end. Diesel or gas, one of the best and easiest things you can do is to try to keep your tank full... Hoping that last sentence will earn me some forgiveness for such a long post.
Good luck.
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